Identification of the Key Factors Related to Bladder Cancer by lncRNA-miRNA-mRNA Three-Layer Network

Abstract

Bladder cancer is the most common malignant tumor of the urinary system, and it has high incidence, high degree of malignancy, and easy recurrence after surgery. The etiology and pathogenesis of bladder cancer are not fully understood, but more and more studies have shown that its development may be regulated by some core molecules. To identify key molecules in bladder cancer, we constructed a three-layer network by merging lncRNA-miRNA regulatory network, miRNA-mRNA regulatory network, and lncRNA-mRNA coexpression network, and further analyzed the topology attributes of the network including the degree, betweenness centrality and closeness centrality of nodes. We found that miRNA-93 and miRNA-195 are controllers for a three-layer network and regulators of numerous target genes associated with bladder cancer. Functional enrichment analysis of their target mRNAs revealed that miRNA-93 and miRNA-195 may be closely related to bladder cancer by disturbing the homeostasis of the cell cycle or HTLV-I infection. In addition, since E2F1 and E2F2 are enriched in various KEGG signaling pathways, we conclude that they are important target genes of miRNA-93, and participate in the apoptotic process by forming a complex with a certain protein or transcription factor activity, sequence-specific DNA binding in bladder cancer. Similarly, AKT3 is an important target gene of miRNA-195, its expression is associated with PI3K-Akt-mTOR signaling pathway and AMPK-mTOR signaling pathway. Therefore, we speculate that AKT3 may participate in proliferation and apoptosis of bladder cancer cells through these pathways, and ultimately affect the biological behavior of tumor cells. Furthermore, through survival analysis, we found that miRNA-195 and miRNA-93 are associated with poor prognosis of bladder cancer. And the Kaplan-Meier curve showed that 24 mRNAs and nine lncRNAs are closely related to overall survival of bladder cancer.

Keywords: TCGA database; bladder cancer; miRNA; three-layer network; topology.

Figure 1

The flowchart of data collection and method implementation.

Figure 2

Differentially expressed RNA in bladder cancer (|logFC| > 1.5 and P-value < 0.05). The Panels (A–C) are the volcano plot of 1457 DElncRNAs, 3047 DEmRNAs (B) and 247 DEmiRNAs. The red denotes upregulations and green denotes downregulations. The x-axis stands for the value of –log10(FDR) and the y-axis stands for the value of logFC.

Figure 3

Three-layer network in bladder cancer. Orange ellipse denotes DElncRNAs, green rectangle denotes DEmRNAs, and yellow triangle denotes DEmiRNAs.

Figure 4

Network related to miRNA-195 and miRNA-93 in bladder cancer. Ellipse represents for DElncRNAs, triangle represents for DEmiRNAs, and rectangle represents for DEmRNAs. Red denotes upregulations; green denotes downregulations.

Figure 5

(A) GO Term of 35 target genes of miRNA-93; (B) GO Term of 36 target genes of miRNA-195.

Figure 6

miRNA-targeted mRNA enrichment pathway. The x-axis represents the genes in the network, in which the red solid line is the target genes of miRNA-93, and the black dotted line is the target genes of miRNA-195. The y-axis represents the KEGG pathway, the red solid box is the enrichment pathway of the miRNA-93 target genes, and the black dotted box is the enrichment pathway of the miRNA-195 target genes.

Figure 7

(A) Survival curves of OS for miRNA-93; (B) Survival curves of OS for miRNA-195. The x-axis denotes the time of OS and y-axis denotes the survival rate.